Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project.
Best, JĂșlia
_Hey JĂșlia!_
If its not of particular interest to all NEST users, but the readers of your paper, I'd just put it up at ModelDB. They give you a permanent link you can use for publication/reference, and just enough space for additional scripts and documentation.
Kind regards,
\Florian
photo *Florian Fiebig, PhD* Researcher Computational Brain Science +46 70-744-7439 tel:+16505426046 | Skype: florianfiebig <#> http://www.numenta.com/ http://us.linkedin.com/in/florian-fiebig-b387b886 Most recent papers:https://rdcu.be/bRLmu https://doi.org/10.1523/JNEUROSCI.1989-16.2016 https://rdcu.be/bRLmu https://www.eneuro.org/content/early/2020/02/28/ENEURO.0374-19.2020
On 11/06/2021 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project.
Best, JĂșlia
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Dear JĂșlia,
do I understand you correctly that your change is really just the addition of some w_min property, get/set_status() handling of it and some conditional code in the weight update function? And am I right in that the behavior of the model currently in NEST would not be changed at all if the new property were set to -infinity by default?
If the answers to these questions are close to âyesâ, I think the best way to integrate your changes into the corresponding built-in modes would be by means of a pull requesthttps://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html against NEST and/or NESTML.
If they are more towards ânoâ or âmaybeâ, I suggest, you come to one of our next open NEST video conferenceshttps://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Conference, so we could discuss more directly.
Cheers, Jochen!
On 11.06.21 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project.
Best, JĂșlia
_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
â
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience JĂŒlich Supercomputing Centre Institute for Advanced Simulation
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Thanks, Florian! Thanks, Jochen!
@Jochen, the answer is mostly "yes" to both your questions. The only thing is that there is already a conditional code in the weight update that sets a minimum value of zero for the weight. I only changed the hardcoded zero to a variable Wmin that can be set with set_status(). So the default value of the property that would lead to no changes in the model behavior in NEST is zero, and not -infinity. But I guess that still counts as a "yes".
I will look into a pull request, then. Thanks!
Cheers, JĂșlia
Em seg., 14 de jun. de 2021 Ă s 12:21, Jochen Martin Eppler < j.eppler@fz-juelich.de> escreveu:
Dear JĂșlia,
do I understand you correctly that your change is really just the addition of some w_min property, get/set_status() handling of it and some conditional code in the weight update function? And am I right in that the behavior of the model currently in NEST would not be changed at all if the new property were set to *-infinity* by default?
If the answers to these questions are close to âyesâ, I think the best way to integrate your changes into the corresponding built-in modes would be by means of a pull request https://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html against NEST and/or NESTML.
If they are more towards ânoâ or âmaybeâ, I suggest, you come to one of our next open NEST video conferences https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Conference, so we could discuss more directly.
Cheers, Jochen!
On 11.06.21 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project.
Best, JĂșlia
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
â
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653
Simulation Laboratory Neuroscience JĂŒlich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi,
I agree with everything Jochen said. The NESTML synapse examples (see, for example, here https://github.com/nest/nestml/pull/655/files#diff-b6340c6dd86cab42c436502a5...) already have a Wmin parameter, so don't need to be adapted. Code generation for the triplet STDP plasticity rule still needs to be improved to account for that edge case we talked about earlier on the list, however: https://github.com/nest/nestml/issues/661 / https://github.com/nest/nest-simulator/issues/1990. Please stay tuned!
Kind regards, Charl
On Mon, Jun 14, 2021, at 14:49, Julia Gallinaro wrote:
Thanks, Florian! Thanks, Jochen!
@Jochen, the answer is mostly "yes" to both your questions. The only thing is that there is already a conditional code in the weight update that sets a minimum value of zero for the weight. I only changed the hardcoded zero to a variable Wmin that can be set with set_status(). So the default value of the property that would lead to no changes in the model behavior in NEST is zero, and not -infinity. But I guess that still counts as a "yes".
I will look into a pull request, then. Thanks!
Cheers, JĂșlia
Em seg., 14 de jun. de 2021 Ă s 12:21, Jochen Martin Eppler j.eppler@fz-juelich.de escreveu:
Dear JĂșlia,
do I understand you correctly that your change is really just the addition of some ` w_min` property, get/set_status() handling of it and some conditional code in the weight update function? And am I right in that the behavior of the model currently in NEST would not be changed at all if the new property were set to *-infinity* by default?
If the answers to these questions are close to âyesâ, I think the best way to integrate your changes into the corresponding built-in modes would be by means of a pull request https://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html against NEST and/or NESTML.
If they are more towards ânoâ or âmaybeâ, I suggest, you come to one of our next open NEST video conferences https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Conference, so we could discuss more directly.
Cheers, Jochen!
On 11.06.21 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It is a minor alteration: I included a minimum hard bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what is the best approach for doing this. Should I provide my copy of the altered model file together with my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on NEST code for a project.
Best, JĂșlia
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
--
Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience JĂŒlich Supercomputing Centre Institute for Advanced Simulation
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org mailto:users%40nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org mailto:users-leave%40nest-simulator.org
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Charl Linssen -
Florian Fiebig -
Jochen Martin Eppler -
Julia Gallinaro